Taxonomic identification report

Sample ID: MP23-0431_rbcL

Department of Agriculture, Fisheries and Forestry logo

[analysis description + link to github repo]

Facility Hogwarts
Analyst John Doe
Analysis started 2025-05-03 01:28:16
Analysis completed 2025-05-03 01:28:16
Wall time 0:0:0 hours

Result overview

Inconclusive

Outcome: The analyst should attempt subjective species identification at the genus level.

Reasoning: [Flag 1C] >3 candidate species matched with high stringency (identity ≥ 98.5%).

Preliminary morphology ID confirmed? NA

Inconclusive taxonomic identity (Flag 1C) Planta.

Taxa of interest detected? True

Flag 2A: Taxon of interest detected in candidate species

Flag 5.1A: The given locus for this taxon is well represented in reference database (>5 entries)

Flag 5.2B: 10-90% of related taxa have reference sequence(s) at the given locus

Sample details

Locus rbcL
Preliminary ID Planta
Taxa of interest Nicotiana tabacum
Country Indonesia
Host NA
Sample ID MP23-0431_rbcL
Query DNA sequence

Analyst evaluation

Identification of candidate species

Flag 1C: The analyst should attempt subjective species identification at the genus level
>3 candidate species matched with high stringency (identity ≥ 98.5%)

Candidate hits must meet ONE of these criteria:

Minimum alignment length 400bp
Minimum query coverage 85.0%

Candidate hits have then been classified as follows:

Classification Alignment identity Number of hits Number of species
STRONG MATCH ≥ 98.5% 499 197
MODERATE MATCH ≥ 93.5% NA NA
NO MATCH < 93.5%

Candidate species

Species Hits Identity E-value Database coverage
Nicotiana sylvestris 2 99.7% 0.0
Nicotiana knightiana 1 99.7% 0.0
Nicotiana tabacum 13 99.7% 0.0
Nicotiana paniculata 1 99.7% 0.0
Nicotiana rustica 1 99.7% 0.0
Nicotiana glauca 2 99.6% 0.0
Nicotiana attenuata 3 99.6% 0.0
Nicotiana suaveolens 1 99.5% 0.0
Nicotiana amplexicaulis 1 99.5% 0.0
Nicotiana benthamiana 1 99.5% 0.0
Anthocercis viscosa 1 99.5% 0.0
Nicotiana debneyi 2 99.5% 0.0
Plastid transformation vector pLEV IR-coS 1 99.5% 0.0
Trompettia cardenasiana 1 99.4% 0.0
Nicotiana acuminata 1 99.4% 0.0
Atropa belladonna 5 99.4% 0.0
Cuscuta compacta 1 99.4% 0.0
Mandragora officinarum 3 99.4% 0.0
Mandragora turcomanica 1 99.4% 0.0
Nicotiana plumbaginifolia 1 99.4% 0.0
Nicotiana obtusifolia 1 99.4% 0.0
Scopolia carniolica 2 99.4% 0.0
Solanum sisymbriifolium 3 99.3% 0.0
synthetic construct 1 99.3% 0.0
Scopolia parviflora 1 99.3% 0.0
Lycianthes radiata 1 99.3% 0.0
Nicotiana undulata 1 99.3% 0.0
Nicotiana tomentosiformis 3 99.3% 0.0
Anisodus luridus 1 99.3% 0.0
Mandragora autumnalis 1 99.3% 0.0
Hyoscyamus niger 2 99.3% 0.0
Physochlaina physaloides 1 99.3% 0.0
Physochlaina orientalis 1 99.3% 0.0
Solandra grandiflora 1 99.3% 0.0
Solanum etuberosum 4 99.2% 0.0
Datura stramonium 9 99.2% 0.0
Przewalskia tangutica 3 99.2% 0.0
Nicandra physalodes 2 99.2% 0.0
Solanaceae sp. YYL-2022 1 99.2% 0.0
Hyoscyamus muticus 1 99.2% 0.0
Solanum palustre 1 99.2% 0.0
Solanum anomalostemon 1 99.2% 0.0
Mandragora caulescens 1 99.2% 0.0
Nicotiana repanda 1 99.1% 0.0
Solanum rostratum 2 99.1% 0.0
Anisodus tanguticus 1 99.1% 0.0
Datura metel 3 99.1% 0.0
Nicotiana stocktonii 1 99.1% 0.0
Solanum sogarandinum 2 99.0% 0.0
Eriolarynx australis 1 99.0% 0.0
Solanum pennellii 4 99.0% 0.0
Iochroma ellipticum 1 99.0% 0.0
Eriolarynx lorentzii 1 99.0% 0.0
Withania sp. 1 99.0% 0.0
Iochroma lehmannii 2 99.0% 0.0
Solanum neorickii 2 99.0% 0.0
Withania adpressa 2 99.0% 0.0
Iochroma umbellatum 1 99.0% 0.0
Solanum huaylasense 1 99.0% 0.0
Saracha punctata 1 99.0% 0.0
Solanum corneliomulleri 1 99.0% 0.0
Solanum peruvianum 2 99.0% 0.0
Solanum chilense 2 99.0% 0.0
Solanum triflorum 1 99.0% 0.0
Withania riebeckii 1 99.0% 0.0
Withania coagulans 3 99.0% 0.0
Iochroma cyaneum 2 99.0% 0.0
Iochroma tingoanum 1 99.0% 0.0
Acnistus arborescens x Iochroma cyaneum 1 99.0% 0.0
Iochroma nitidum 1 99.0% 0.0
Nolana spathulata 1 99.0% 0.0
Eriolarynx fasciculata 1 99.0% 0.0
Nicotiana otophora 1 99.0% 0.0
Solanum lycopersicoides 1 99.0% 0.0
Saracha nigribaccata 1 99.0% 0.0
Solanum arcanum 2 99.0% 0.0
Iochroma salpoanum 1 99.0% 0.0
Anisodus acutangulus 2 99.0% 0.0
Solanum aligerum 1 99.0% 0.0
Dunalia obovata 1 99.0% 0.0
Solanum chmielewskii 1 99.0% 0.0
Solanum anamatophilum 1 99.0% 0.0
Iochroma stenanthum 1 99.0% 0.0
Solanum habrochaites 5 99.0% 0.0
Atropanthe sinensis 1 99.0% 0.0
Solanum sitiens 1 99.0% 0.0
Solanum nitidum 1 99.0% 0.0
Iochroma loxense 1 99.0% 0.0
Acnistus arborescens 1 99.0% 0.0
Trozelia umbellata 1 99.0% 0.0
Discopodium penninervium 1 99.0% 0.0
Withania somnifera 4 99.0% 0.0
Nolana albescens 1 99.0% 0.0
Lycium pallidum 1 99.0% 0.0
Vassobia dichotoma 1 99.0% 0.0
Solanum medians 10 98.8% 0.0
Solanum canasense 9 98.8% 0.0
Solanum x curtilobum 1 98.8% 0.0
Solanum morelliforme 2 98.8% 0.0
Jaltomata sinuosa 1 98.8% 0.0
Solanum bulbocastanum 7 98.8% 0.0
Solanum andreanum 3 98.8% 0.0
Solanum berthaultii 1 98.8% 0.0
Solanum phureja 5 98.8% 0.0
Solanum stenotomum 4 98.8% 0.0
Solanum tuberosum 12 98.8% 0.0
Solanum wittmackii 2 98.8% 0.0
Solanum boliviense 3 98.8% 0.0
Solanum chomatophilum 11 98.8% 0.0
Solanum multiinterruptum 9 98.8% 0.0
Solanum albornozii 2 98.8% 0.0
Solanum acroglossum 2 98.8% 0.0
Solanum marinasense 3 98.8% 0.0
Solanum bukasovii 15 98.8% 0.0
Solanum cajamarquense 3 98.8% 0.0
Solanum cardiophyllum 3 98.8% 0.0
Solanum ambosinum 5 98.8% 0.0
Solanum megistacrolobum 5 98.8% 0.0
Solanum raphanifolium 8 98.8% 0.0
Solanum chiquidenum 3 98.8% 0.0
Solanum piurae 2 98.8% 0.0
Solanum jamesii 4 98.8% 0.0
Solanum candolleanum 11 98.8% 0.0
Solanum paucissectum 3 98.8% 0.0
Solanum tarnii x Solanum tuberosum 1 98.8% 0.0
Solanum x juzepczukii 3 98.8% 0.0
Solanum aculeatissimum 2 98.8% 0.0
Solanum trifidum 1 98.8% 0.0
Solanum pinnatisectum 4 98.8% 0.0
Schraderanthus viscosus 1 98.8% 0.0
Solanum limbaniense 1 98.8% 0.0
Solanum lignicaule 4 98.8% 0.0
Solanum leptophyes 5 98.8% 0.0
Solanum ehrenbergii 1 98.8% 0.0
Lycium ferocissimum 4 98.8% 0.0
Physalis virginiana 1 98.8% 0.0
Solanum stenophyllidium 3 98.8% 0.0
Solanum acaule 5 98.8% 0.0
Solanum achacachense 1 98.8% 0.0
Solanum x blanco-galdosii 1 98.8% 0.0
Solanum stipuloideum 1 98.8% 0.0
Solanum hypacrarthrum 1 98.8% 0.0
Solanum tacnaense 2 98.8% 0.0
Oryctes nevadensis 1 98.8% 0.0
Solanum huancabambense 1 98.8% 0.0
Solanum abancayense 1 98.8% 0.0
Dunalia brachyacantha 1 98.8% 0.0
Solanum trisectum 1 98.8% 0.0
Solanum humectophilum 1 98.8% 0.0
Withania frutescens 1 98.8% 0.0
Solanum tarapatanum 1 98.8% 0.0
Solanum ahanhuiri 2 98.8% 0.0
Solanum augustii 1 98.8% 0.0
Solanum gracilifrons 1 98.8% 0.0
Solanum infundibuliforme 2 98.8% 0.0
Solanum acroscopicum 1 98.8% 0.0
Solanum dolichocremastrum 1 98.8% 0.0
Physalis peruviana 3 98.8% 0.0
Solanum pachyandrum 1 98.8% 0.0
Solanum lycopersicum 48 98.7% 0.0
Solanum polyadenium 3 98.7% 0.0
Physalis philadelphica 2 98.7% 0.0
Solanum ochranthum 1 98.7% 0.0
Solanum gourlayi 7 98.7% 0.0
Nicotiana sp. SH-2010 1 98.7% 0.0
Physalis cordata 1 98.7% 0.0
Solanum pimpinellifolium 7 98.7% 0.0
Solanum capsicoides 2 98.7% 0.0
Solanum sparsipilum 5 98.7% 0.0
Solanum brevicaule 12 98.7% 0.0
Solanum salicifolium 2 98.7% 0.0
Solanum cantense 2 98.7% 0.0
Solanum paposanum 1 98.7% 0.0
Solanum brachyantherum 1 98.7% 0.0
Solanum incamayoense 5 98.7% 0.0
Solanum tweedianum 1 98.7% 0.0
Physalis ixocarpa 1 98.7% 0.0
Solanum virginianum 1 98.7% 0.0
Solanum annuum 1 98.7% 0.0
Solanum lesteri 1 98.7% 0.0
Solanum salamancae 1 98.7% 0.0
Salpiglossis sinuata 1 98.7% 0.0
Jaltomata bicolor 1 98.7% 0.0
Physalis minima 1 98.7% 0.0
Physalis pruinosa 1 98.7% 0.0
Solanum remyanum 1 98.7% 0.0
Solanum galapagense 2 98.7% 0.0
Solanum aureum 1 98.7% 0.0
Solanum mochiquense 2 98.7% 0.0
Physalis ampla 1 98.7% 0.0
Physalis angulata 3 98.7% 0.0
Physalis sp. SH-2010 1 98.7% 0.0
Solanum cheesmaniae 1 98.7% 0.0
Physalis longifolia 1 98.7% 0.0
Brugmansia arborea 1 98.7% 0.0
Solanum sanchez-vegae 1 98.7% 0.0
Solanum microdontum 1 98.7% 0.0

Boxplot of BLAST hit identity percent grouped by genus

The boxplot above shows the distribution of BLAST hits identity within each genus. Each data point shows the alignment identity between the query sequence and reference sequence. The analyst may wish to refer to this figure when making a subjective genus-level identification for the sample.

Analyst evaluation

Taxa of interest (TOI)

This sections shows the taxa of interest (TOI) specified by the sample submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.

Taxon of interest Match rank Match taxon Match species Match accession Match identity Database coverage
Nicotiana tabacum species Nicotiana tabacum Nicotiana tabacum AP019624 0.997

Reference sequence source diversity

This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.

Analyst evaluation

No candidate species to report on.

Intraspecies diversity

This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.

Analyst evaluation

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The phylogetic tree was constructed with FastME using the Neighbor-Joining method. Multiple-sequence alignment of the candidate reference sequences was performed using MAFFT. The visualization is rendered with TidyTree.

Taxonomy Check

The following resources can be used to ensure that the given taxonomy is legitimate and current.

Taxa Database
General GBIF
General ITIS
Mealybugs & scale ScaleNet database
Thrips Thripswiki
Spider Mites Spider Mites Database
Psocodea (Barklice, Booklice, and Parasitic Lice) Psocodea Species File Online
Orthoptera Orthoptera Species File Online
Drosophilidae TaxoDros
Diptera Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum
Aphids Aphid Species File
Ants AntWeb
AntCat
Lepidoptera (butterflies and moths) The Global Lepidoptera Names Index
Gracillariidae (primitive moths) Global Taxonomic Database of Gracillariidae
Pyralidae (pyralid moths) Global Information System on Pyraloidea
Tortricidae (tortrix moths) Tortricidae Resources on the Net